To explain the issue,I've setup 2 raid sets from the raid setup screen on bootup on the Hitachi's and the Seagates. One raid set is a backup of the other so obviously this is quite important to me.

After reinstalling Windows these are no longer recognized. At first all 4 disks were visible individually and windows was popping up chkdsk on bootup, which ive cancelled each time.

After installing the latest driver from intel (RST, same version was installed before reinstallation) I now get to see the 2 raid disks of the correct size but they are showing as RAW. Windows wants to initialize the disks. Next to that there are 2 disks with the same sizes as the raw disks with a partition and drive letter, but they are inaccessible. Windows wants to format the disks. I've removed the drive letter from these drives to prevent issues with programs wanting to access them.

Windows Disk Manager is giving me the option between MBR and GPT upon initializing the disks and advises to use GPT for >2TB drives. Both volumes are over 2TB but when I choose either option it pops up a message saying the "system cannot find the file specified". Also I am not sure whether I've used MBR or GPT previously but both give the error message.